In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement
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We present an implementation of an in vitro signal recorder based on DNA assembly and strand displacement. The signal recorder implements a stack data structure in which both data as well as operators are represented by single stranded DNA “bricks”. The stack grows by adding push and write bricks and shrinks in last-in-first-out manner by adding pop and read bricks. We report the design of the signal recorder and its mode of operations and give experimental results from capillary electrophoresis as well as transmission electron microscopy that demonstrate the capability of the device to store and later release several successive signals. We conclude by discussing potential future improvements of our current results.
KeywordsMigration Time Structural Hairpin Strand Displacement Branch Migration Runaway Process
This work has been supported by EPSRC grant agreements no EP/J004111/1, EP/J004111/2, EP/L001489/1, EP/L001489/2. We thank Chien-yi Chang, Christoph Flamm, Alessandro Ceccarelli, Omer Markovitch, and Ben Shirt-Ediss for helpful discussions.
- 13.Terrazas, G., Gheorghe, M., Kendall, G., Krasnogor, N.: Evolving tiles for automated self-assembly design. In: IEEE Congress on Evolutionary Computation, CEC 2007, pp. 2001–2008 (2007)Google Scholar
- 16.Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., Hofacker, I.L.: ViennaRNA Package 2.0. Algorithms. Mol. Biol. 6(1), 26 (2011)Google Scholar
- 18.Hadorn, M., Bnzli, E., Fellermann, H., Eggenberger Hotz, P., Hanczyc, M.: Specific and reversible DNA-directed self-assembly of emulsion droplets. Proc. Nat. Acad. Sci. USA 109(47) (2012)Google Scholar